Maybe the duplicate is added by "something else"?
For example, for a Gmail account, there is a setting (in web mail) to automatically add any incoming appointments, it is enabled by default, and to my knowledge, works independently of any mail app (entirely on Google's side).
What sort of mail account are you seeing this in? Gmail, something else, such as your corporate account?
Things I'd check:
1 - Calendar app, when you see duplicates, there is a way to see (for each, if you open them individually), what "account" on the phone they're under.
2 - Phone settings -> accounts. Are there any accounts that could be syncing your appointments? For Gmail, see above, but maybe a corporate account set up in another app (mail, calendar, sometimes those can connect directly to your account's servers)?